Hello, The data I am finding matches exactly between the Yeast assembly browser, Table browser and download text files. The off-by-one-base coordinate and reverse strand coordinate details are explained in these help sections: (perhaps they are what is causing the confusion): http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 http://genome.ucsc.edu/FAQ/FAQtracks#tracks15 http://genome.ucsc.edu/FAQ/FAQformat#format9
We already covered the details of what I found in the Yeast assembly browser for the SGD track, but here are the results for the Ensembl track and the other data sources for comparison: --- Using Yeast assembly browser: position search by "YMR280C", click on result name to go to the details page: Ensembl Gene Predictions (YMR280C - Ensembl 52) Ensembl Gene Link: YMR280C Ensembl Transcript: YMR280C Ensembl Protein: YMR280C Position: chr13:827027-831328 Genomic Size: 4302 Strand: - Alternate Name: YMR280C CDS Start: complete CDS End: complete --- Using ftp to our downloads server to get the file ensGene.txt in the current state and grep the example gene, I get this: $ grep YMR280C ensGene.txt 591 YMR280C chr13 - 827026 831328 827026 831328 1 827026, 831328, 0 YMR280C cmpl cmpl 0, --- Using Table Browser, and select the yeast genome, track, and table to also be ensGene, and add a filter using the example gene name I get this: #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames 591 YMR280C chr13 - 827026 831328 827026 831328 1 827026, 831328, 0 YMR280C cmpl cmpl 0, If I have misunderstood your question again, please provide exact details about how your are obtaining the data you feel to be inconsistent. Thanks you, Jennifer Jackson UCSC Genome Bioinformatics Group > Hi, > This is alright. I was not talking about the annotation on the > browser. I was asking about the annotation at *ensGene.txt* file that > is provided in the annotation page of yeast genome(Downloads -> SacCer > -> Annotation database > (http://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/database/). Here, > the annotation (start and end position) does not match the position of > the genes found by searching in the Browser (e.g., YMR280C, YNL177C). > So I was asking whether you have any updated file for annotation. > > Thanking you > Sincerely, > Riddhiman Dhar _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
